Amino Acid 3D Explorer

What are the 20 standard amino acids and their functional groups?

The 20 standard amino acids share a core backbone: a central alpha-carbon carrying an amino group (−NH₂, or in proline a ring −NH−), a carboxyl group (−COOH), a hydrogen atom and a distinguishing side chain (R group). They are categorised into non-polar aliphatic, aromatic, polar uncharged, positively charged (basic: Lys, Arg, His), and negatively charged (acidic: Asp, Glu) residues.

The 20 amino acids and their side chains

The side chain is the only part that differs, and it decides the class. Lehninger’s textbook sorts the 20 into five classes: 7 nonpolar and aliphatic, 3 aromatic, 5 polar and uncharged, 3 positively charged and 2 negatively charged. The chart opens in that order, each card topped with its class colour.

pK₁ belongs to the α-carboxyl group, pK₂ to the α-amino group and pKR to the side chain, from Nelson and Cox, Lehninger Principles of Biochemistry, 7th edition, Table 3-1. Each charge is the explorer’s own, computed group by group.

Each amino acid has a page of its own, with its charge from pH 1 to 13 and its pI worked out: see the amino acid pKa and pI table.

Using the explorer

• The chart shows all 20 in 3D at one scale, so tryptophan is as much bigger than glycine as it really is. It opens with a sweep of the pH from 7.4 down to 1, up to 13 and back, and each card’s badge changes as its groups gain and lose protons. Press Sweep pH to run it again. With reduced motion set, it opens still, at pH 7.4.
• The pH slider, beside Play and Sweep pH, sets the pH for everything at once. The marks under it are blood plasma’s 7.4 and the pKa values and pI of the amino acid the readouts describe, and its track is blue where that amino acid is net positive and red where it is net negative, as the plot is.
• Tap a card, or choose from the Amino acid menu, to open it. Drag to turn it, and tap an atom to name it. A proton that comes and goes is drawn as faint as the share of molecules that have it, and each charged group glows blue for positive and red for negative, as strongly as it is charged.
• Hydrogens, Labels, Space-filling and D form, under an open amino acid, change how it is drawn, and the Plot menu switches the plot between net charge against pH and the titration curve. On a wide screen the stage also adds up its charge group by group, beside the molecule.
• Save image saves the chart or the molecule as it is, with the pH in the picture.

Worked example: histidine from pH 1 to 13

Histidine has three groups that ionise: its α-carboxyl, pK₁ = 1.82, its imidazole side chain, pKR = 6.00, and its α-amino group, pK₂ = 9.17. For each, the Henderson-Hasselbalch equation gives the share of molecules in which it carries its proton. At pH 7.4:

• α-carboxyl: deprotonated in 1/(1 + 10^(1.82 − 7.4)) of molecules, which is 1.0000 to four places, so it contributes −1.0000.
• α-amino: protonated in 1/(1 + 10^(7.4 − 9.17)) = 0.9833, contributing +0.9833.
• Imidazole: protonated in 1/(1 + 10^(7.4 − 6.00)) = 1/(1 + 25.1) = 0.0383, contributing +0.0383.
• Net charge: 0.9833 + 0.0383 − 1.0000 = +0.0216, which the badge rounds to +0.02.

Sweep the pH and the same sum gives +1.87 at pH 1, where most molecules carry both ring protons and the carboxyl proton, +1.00 at pH 4, +0.50 at pH 6.00, where half the side chains are protonated, 0.00 at the pI, 7.59, −0.50 at pH 9.17 and −1.00 at pH 13. The pI is the mean of the two pKas either side of the neutral form, (6.00 + 9.17)/2 ≈ 7.59.

The isoelectric point and the tyrosine exception

The pI is the pH at which an amino acid carries no net charge, so it does not move in an electric field. For an amino acid with two ionisable groups it is the mean of their pKas: glycine’s is (2.34 + 9.60)/2 = 5.97. With a third group, take the two pKas either side of the neutral form. Aspartic acid’s neutral form lies between its two carboxyls, so its pI is (1.88 + 3.65)/2 ≈ 2.77; lysine’s lies between its two amino groups, so its pI is (8.95 + 10.53)/2 = 9.74.

The explorer also finds, by bisection, the pH where its own net charge curve crosses zero. For 19 amino acids that agrees with the table to within 0.01. Tyrosine is the exception: 5.63 against the table’s 5.66, and here the table is right. A titration measures each pKa for the molecule as a whole, so tyrosine’s α-amino pKa, 9.11, already counts the few molecules whose phenol, pKR 10.07, gives up its proton first. The explorer treats each group on its own and adds the phenol on top: at pH 5.66 about 4 in 100,000 of its phenols are ionised, beside the 35 in 100,000 that have lost an α-amino proton, so it counts about a tenth too many negative molecules. The net charge curve is so flat there that this moves the zero crossing by 0.02. The pI readout gives the table’s 5.66, with the curve’s 5.63 beside it.

Titration curves

Switch the plot to the titration curve to see pH against the equivalents of OH⁻ added, starting from the fully protonated amino acid at pH 0, as MCAT courses draw it. Each pKa is a flat stretch, a buffer region, where the pH is the pKa with that group half titrated. Between two of them the curve climbs steeply, and the pI sits in the middle of that climb: at about 1.00 equivalent for glycine, of the 2.00 it takes to go from pH 0 to 14. An amino acid with an ionisable side chain takes about 3 equivalents and has three flat stretches.

For one group at a time, the Henderson-Hasselbalch calculator gives the ratio of acid to base at any pH, and the titration curve calculator draws the curve for a weak acid titrated with a strong base, volumes and all.

L, S and the cysteine exception

Every amino acid except glycine has four different groups on its α-carbon, so it has two mirror-image forms, L and D, and proteins are built from L amino acids only. Press D form under an open amino acid to see the mirror image. By the Cahn-Ingold-Prelog rules, 18 of the 19 chiral amino acids are S at the α-carbon, because NH₂ outranks COOH, which outranks the side chain. Cysteine is R: the sulfur in its CH₂SH outranks the oxygens of COOH, so the side chain ranks second, and the letter changes while the shape does not. Isoleucine and threonine have a second stereocentre, at Cβ: L-isoleucine is (2S,3S) and L-threonine (2S,3R). The R and S Configuration Explorer ranks the groups step by step.

Hydrophobicity

The Hydropathy readout is Kyte and Doolittle’s scale. Isoleucine, at 4.5, valine, 4.2, and leucine, 3.8, are the most hydrophobic; arginine, at −4.5, is the most hydrophilic, then lysine at −3.9. Hydrophobic side chains gather inside a folded protein and line the parts of membrane proteins that cross the membrane, and the space-filling view shows how much room each one takes up.

From codons to side chains

The genetic code has 61 codons for the 20 amino acids, so most have more than one. Leucine, serine and arginine have 6 each; methionine and tryptophan have 1 each. The Codons readout lists them as mRNA reads them. The DNA to Protein Translator turns a sequence into its amino acids, and the Protein Synthesis Simulator builds the chain on a ribosome, its beads in these class colours.

What this model leaves out

• Groups that affect each other. Each group is treated as ionising independently, the standard textbook treatment. In reality a charge on one group nudges the pKa of its neighbours, so the shares of the rarer protonation states are only approximate, and the measured pKas belong to the whole molecule, which is why tyrosine’s curve crosses zero at 5.63 rather than at its pI, 5.66.
• The rest of the protein. These are free amino acids. In a protein the α-amino and α-carboxyl groups are tied up in peptide bonds, except at the two ends, and a side chain’s pKa can shift by a unit or more with its surroundings.
• Other conformations. Each amino acid is one idealised conformer, from the wwPDB Chemical Component Dictionary, not the commonest arrangement of its side chain in proteins. The model places the α-amino hydrogens itself, as a regular tetrahedron, and draws every other atom where the dictionary puts it.
• One table. The pKa values are those of one table, for free amino acids in water. Other tables round them or give them for other temperatures and salt concentrations.

Common mistakes

• Averaging all three pKas. For lysine that gives (2.18 + 8.95 + 10.53)/3 = 7.22, but its pI is 9.74, the mean of the two pKas either side of its neutral form.
• Treating histidine as positive at pH 7.4. It is filed with the positive amino acids, but at pH 7.4 only about 4 percent of its side chains carry the proton, and its net charge is +0.02.
• Treating cysteine as neutral. Its thiol, pKR 8.18, is about 14 percent ionised at pH 7.4, so cysteine carries −0.14.
• Mixing up L with S. L and D name the arrangement; R and S come from ranking the groups. L-cysteine is R.
• Drawing the uncharged form. In water an amino acid near its pI is almost entirely the zwitterion, NH₃⁺ and COO⁻, not NH₂ and COOH: 99.4 percent of glycine at pH 7.4.

Where the numbers come from

The 3D coordinates are the ideal coordinates of the wwPDB Chemical Component Dictionary (Westbrook et al. (2015), Bioinformatics 31:1274), made available under the CC0 1.0 Universal Public Domain Dedication. Its backbone bond lengths agree with the values Engh and Huber (1991) set for protein structures to within 0.03 Å. The pKa values and pIs are from Nelson and Cox, Lehninger Principles of Biochemistry, 7th edition, Table 3-1, hydropathy from Kyte and Doolittle (1982), the space-filling radii from Bondi (1964), and the molar masses from the IUPAC standard atomic weights.